Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis-met...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-07-01
|
| Series: | PLoS Genetics |
| Online Access: | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1006141&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849467669967798272 |
|---|---|
| author | Dazhe Meng Manu Dubin Pei Zhang Edward J Osborne Oliver Stegle Richard M Clark Magnus Nordborg |
| author_facet | Dazhe Meng Manu Dubin Pei Zhang Edward J Osborne Oliver Stegle Richard M Clark Magnus Nordborg |
| author_sort | Dazhe Meng |
| collection | DOAJ |
| description | The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis-methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs. |
| format | Article |
| id | doaj-art-aec992b6620f4a53a622866432e35b3a |
| institution | Kabale University |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2016-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-aec992b6620f4a53a622866432e35b3a2025-08-20T03:26:09ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042016-07-01127e100614110.1371/journal.pgen.1006141Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.Dazhe MengManu DubinPei ZhangEdward J OsborneOliver StegleRichard M ClarkMagnus NordborgThe extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis-methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1006141&type=printable |
| spellingShingle | Dazhe Meng Manu Dubin Pei Zhang Edward J Osborne Oliver Stegle Richard M Clark Magnus Nordborg Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana. PLoS Genetics |
| title | Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana. |
| title_full | Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana. |
| title_fullStr | Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana. |
| title_full_unstemmed | Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana. |
| title_short | Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana. |
| title_sort | limited contribution of dna methylation variation to expression regulation in arabidopsis thaliana |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1006141&type=printable |
| work_keys_str_mv | AT dazhemeng limitedcontributionofdnamethylationvariationtoexpressionregulationinarabidopsisthaliana AT manudubin limitedcontributionofdnamethylationvariationtoexpressionregulationinarabidopsisthaliana AT peizhang limitedcontributionofdnamethylationvariationtoexpressionregulationinarabidopsisthaliana AT edwardjosborne limitedcontributionofdnamethylationvariationtoexpressionregulationinarabidopsisthaliana AT oliverstegle limitedcontributionofdnamethylationvariationtoexpressionregulationinarabidopsisthaliana AT richardmclark limitedcontributionofdnamethylationvariationtoexpressionregulationinarabidopsisthaliana AT magnusnordborg limitedcontributionofdnamethylationvariationtoexpressionregulationinarabidopsisthaliana |